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libcifpp
Commit ba2b06f5 by Maarten L. Hekkelman
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reduce complexity

parent fecc762d
Showing with 40 additions and 348 deletions
changelog
Version 4.0.0
- getResidue in mmcif::Structure now requires both a
sequence ID and an auth sequence ID. Very unfortunate.
sequence ID and an auth sequence ID. As a result the code was cleaned
up considerably.
Version 3.0.5
- mmcif::Structure redesign. It is now a wrapper around a cif::Datablock.
......
include/cif++/Structure.hpp
......@@ -661,26 +661,6 @@ class Structure
return getResidue(atom.labelAsymID(), atom.labelCompID(), atom.labelSeqID(), atom.authSeqID());
}
// map between auth and label locations
std::tuple<std::string, int, std::string> MapAuthToLabel(const std::string &asymID,
const std::string &seqID, const std::string &compID, const std::string &insCode = "");
std::tuple<std::string, std::string, std::string, std::string> MapLabelToAuth(
const std::string &asymID, int seqID, const std::string &compID);
// returns chain, seqnr, icode
std::tuple<char, int, char> MapLabelToAuth(
const std::string &asymID, int seqID) const;
// returns chain,seqnr,comp,iCode
std::tuple<std::string, int, std::string, std::string> MapLabelToPDB(
const std::string &asymID, int seqID, const std::string &compID,
const std::string &authSeqID) const;
std::tuple<std::string, int, std::string> MapPDBToLabel(
const std::string &asymID, int seqID, const std::string &compID, const std::string &iCode) const;
// Actions
void removeAtom(Atom &a);
void swapAtoms(Atom &a1, Atom &a2); // swap the labels for these atoms
......@@ -755,22 +735,18 @@ class Structure
private:
friend Polymer;
friend Residue;
// friend residue_view;
// friend residue_iterator;
std::string insertCompound(const std::string &compoundID, bool isEntity);
std::string createEntityForBranch(Branch &branch);
void loadData();
void updateAtomIndex();
void loadAtomsForModel(StructureOpenOptions options);
cif::Datablock &mDb;
size_t mModelNr;
AtomView mAtoms;
std::vector<size_t> mAtomIndex;
std::list<Polymer> mPolymers;
std::list<Branch> mBranches;
std::vector<Residue> mNonPolymers;
......
src/CifParser.cpp
......@@ -96,7 +96,7 @@ bool isUnquotedString(const char *s)
// but be careful it does not contain e.g. stop_
if (result)
{
const std::regex reservedRx(R"(^(?:data|save|loop|stop|global)_.+)", std::regex_constants::icase);
const std::regex reservedRx(R"((^(?:data|save)|.*(?:loop|stop|global))_.+)", std::regex_constants::icase);
result = not std::regex_match(ss, reservedRx);
}
......
src/Structure.cpp
......@@ -420,18 +420,8 @@ std::string Residue::authInsCode() const
assert(mStructure);
std::string result;
try
{
char iCode;
tie(std::ignore, std::ignore, iCode) = mStructure->MapLabelToAuth(mAsymID, mSeqID);
result = std::string{iCode};
ba::trim(result);
}
catch (...)
{
}
if (not mAtoms.empty())
result = mAtoms.front().get_property<std::string>("PDB_ins_code");
return result;
}
......@@ -441,15 +431,8 @@ std::string Residue::authAsymID() const
assert(mStructure);
std::string result;
try
{
tie(result, std::ignore, std::ignore) = mStructure->MapLabelToAuth(mAsymID, mSeqID);
}
catch (...)
{
result = mAsymID;
}
if (not mAtoms.empty())
result = mAtoms.front().get_property<std::string>("auth_asym_id");
return result;
}
......@@ -574,25 +557,7 @@ bool Residue::isEntity() const
std::string Residue::authID() const
{
std::string result;
try
{
char chainID, iCode;
int seqNum;
std::tie(chainID, seqNum, iCode) = mStructure->MapLabelToAuth(mAsymID, mSeqID);
result = chainID + std::to_string(seqNum);
if (iCode != ' ' and iCode != 0)
result += iCode;
}
catch (...)
{
result = mAsymID + std::to_string(mSeqID);
}
return result;
return authAsymID() + authSeqID() + authInsCode();
}
std::string Residue::labelID() const
......@@ -1425,8 +1390,6 @@ Structure::~Structure()
void Structure::loadData()
{
updateAtomIndex();
auto &polySeqScheme = category("pdbx_poly_seq_scheme");
for (auto &r : polySeqScheme)
......@@ -1509,16 +1472,6 @@ void Structure::loadData()
}
}
void Structure::updateAtomIndex()
{
mAtomIndex = std::vector<size_t>(mAtoms.size());
iota(mAtomIndex.begin(), mAtomIndex.end(), 0);
sort(mAtomIndex.begin(), mAtomIndex.end(), [this](size_t a, size_t b)
{ return mAtoms[a].id() < mAtoms[b].id(); });
}
void Structure::sortAtoms()
{
sort(mAtoms.begin(), mAtoms.end(), [](auto &a, auto &b)
......@@ -1530,8 +1483,6 @@ void Structure::sortAtoms()
atom.setID(id);
++id;
}
updateAtomIndex();
}
AtomView Structure::waters() const
......@@ -1565,28 +1516,13 @@ AtomView Structure::waters() const
Atom Structure::getAtomByID(std::string id) const
{
auto i = std::lower_bound(mAtomIndex.begin(), mAtomIndex.end(),
id, [this](auto &a, auto &b)
{ return mAtoms[a].id() < b; });
// auto i = find_if(mAtoms.begin(), mAtoms.end(),
// [&id](auto& a) { return a.id() == id; });
Atom result;
if (i == mAtomIndex.end() or mAtoms[*i].id() != id)
for (auto &atom : mAtoms)
{
auto j = std::find_if(mAtoms.begin(), mAtoms.end(), [id](const Atom &a) { return a.id() == id; });
if (j == mAtoms.end())
throw std::out_of_range("Could not find atom with id " + id);
result = *j;
if (atom.id() == id)
return atom;
}
else
result = mAtoms[*i];
return result;
throw std::out_of_range("Could not find atom with id " + id);
}
Atom Structure::getAtomByLabel(const std::string &atomID, const std::string &asymID, const std::string &compID, int seqID, const std::string &altID)
......@@ -1747,248 +1683,6 @@ Residue &Structure::getResidue(const std::string &asymID, const std::string &com
throw std::out_of_range("Could not find residue " + asymID + '/' + std::to_string(seqID) + '-' + authSeqID);
}
// Residue &Structure::getResidue(const mmcif::Atom &atom)
// {
// using namespace cif::literals;
// auto asymID = atom.labelAsymID();
// auto entityID = atom.labelEntityID();
// auto type = mDb["entity"].find1<std::string>("id"_key == entityID, "type");
// if (type == "water")
// {
// auto authSeqID = atom.authSeqID();
// for (auto &res : mNonPolymers)
// {
// if (res.asymID() != asymID or res.authSeqID() != authSeqID)
// continue;
// return res;
// }
// throw std::out_of_range("Could not find water " + asymID + '/' + authSeqID);
// }
// else if (type == "branched")
// {
// auto authSeqID = std::stoi(atom.authSeqID());
// for (auto &branch : mBranches)
// {
// if (branch.asymID() != asymID)
// continue;
// for (auto &sugar : branch)
// {
// if (sugar.asymID() == asymID and sugar.num() == authSeqID)
// return sugar;
// }
// }
// throw std::out_of_range("Could not find sugar residue " + asymID + '/' + std::to_string(authSeqID));
// }
// else if (type == "polymer")
// {
// auto seqID = atom.labelSeqID();
// for (auto &poly : mPolymers)
// {
// if (poly.asymID() != asymID)
// continue;
// for (auto &res : poly)
// {
// if (res.seqID() == seqID)
// return res;
// }
// }
// throw std::out_of_range("Could not find residue " + asymID + '/' + std::to_string(seqID));
// }
// for (auto &res : mNonPolymers)
// {
// if (res.asymID() != asymID)
// continue;
// return res;
// }
// throw std::out_of_range("Could not find residue " + asymID);
// }
std::tuple<char, int, char> Structure::MapLabelToAuth(
const std::string &asymID, int seqID) const
{
auto &db = datablock();
std::tuple<char, int, char> result;
bool found = false;
for (auto r : db["pdbx_poly_seq_scheme"].find(
cif::Key("asym_id") == asymID and
cif::Key("seq_id") == seqID))
{
std::string auth_asym_id, pdb_ins_code, pdb_seq_num, auth_seq_num;
cif::tie(auth_asym_id, auth_seq_num, pdb_seq_num, pdb_ins_code) =
r.get("pdb_strand_id", "auth_seq_num", "pdb_seq_num", "pdb_ins_code");
if (auth_seq_num.empty())
auth_seq_num = pdb_seq_num;
try
{
result = std::make_tuple(auth_asym_id.front(), std::stoi(auth_seq_num),
pdb_ins_code.empty() ? ' ' : pdb_ins_code.front());
}
catch (const std::exception &ex)
{
result = std::make_tuple(auth_asym_id.front(), 0,
pdb_ins_code.empty() ? ' ' : pdb_ins_code.front());
}
found = true;
break;
}
if (not found)
{
auto r = db["pdbx_nonpoly_scheme"].find(cif::Key("asym_id") == asymID);
if (r.size() == 1)
{
std::string pdb_strand_id, pdb_ins_code;
int pdb_seq_num;
cif::tie(pdb_strand_id, pdb_seq_num, pdb_ins_code) =
r.front().get("pdb_strand_id", "pdb_seq_num", "pdb_ins_code");
result = std::make_tuple(pdb_strand_id.front(), pdb_seq_num,
pdb_ins_code.empty() ? ' ' : pdb_ins_code.front());
found = true;
}
}
if (not found)
{
auto r = db["pdbx_"].find(cif::Key("asym_id") == asymID);
if (r.size() == 1)
{
std::string pdb_strand_id, pdb_ins_code;
int pdb_seq_num;
cif::tie(pdb_strand_id, pdb_seq_num, pdb_ins_code) =
r.front().get("pdb_strand_id", "pdb_seq_num", "pdb_ins_code");
result = std::make_tuple(pdb_strand_id.front(), pdb_seq_num,
pdb_ins_code.empty() ? ' ' : pdb_ins_code.front());
found = true;
}
}
return result;
}
std::tuple<std::string, int, std::string, std::string> Structure::MapLabelToPDB(
const std::string &asymID, int seqID, const std::string &monID,
const std::string &authSeqID) const
{
auto &db = datablock();
std::tuple<std::string, int, std::string, std::string> result;
if (monID == "HOH")
{
for (auto r : db["pdbx_nonpoly_scheme"].find(
cif::Key("asym_id") == asymID and
cif::Key("pdb_seq_num") == authSeqID and
cif::Key("mon_id") == monID))
{
result = r.get("pdb_strand_id", "pdb_seq_num", "pdb_mon_id", "pdb_ins_code");
break;
}
}
else
{
for (auto r : db["pdbx_poly_seq_scheme"].find(
cif::Key("asym_id") == asymID and
cif::Key("seq_id") == seqID and
cif::Key("mon_id") == monID))
{
result = r.get("pdb_strand_id", "pdb_seq_num", "pdb_mon_id", "pdb_ins_code");
break;
}
for (auto r : db["pdbx_nonpoly_scheme"].find(
cif::Key("asym_id") == asymID and
cif::Key("mon_id") == monID))
{
result = r.get("pdb_strand_id", "pdb_seq_num", "pdb_mon_id", "pdb_ins_code");
break;
}
}
return result;
}
std::tuple<std::string, int, std::string> Structure::MapPDBToLabel(const std::string &asymID, int seqID,
const std::string &compID, const std::string &iCode) const
{
auto &db = datablock();
std::tuple<std::string, int, std::string> result;
if (iCode.empty())
{
for (auto r : db["pdbx_poly_seq_scheme"].find(
cif::Key("pdb_strand_id") == asymID and
cif::Key("pdb_seq_num") == seqID and
cif::Key("pdb_mon_id") == compID and
cif::Key("pdb_ins_code") == cif::Empty()))
{
result = r.get("asym_id", "seq_id", "mon_id");
break;
}
for (auto r : db["pdbx_nonpoly_scheme"].find(
cif::Key("pdb_strand_id") == asymID and
cif::Key("pdb_seq_num") == seqID and
cif::Key("pdb_mon_id") == compID and
cif::Key("pdb_ins_code") == cif::Empty()))
{
result = r.get("asym_id", "ndb_seq_num", "mon_id");
break;
}
}
else
{
for (auto r : db["pdbx_poly_seq_scheme"].find(
cif::Key("pdb_strand_id") == asymID and
cif::Key("pdb_seq_num") == seqID and
cif::Key("pdb_mon_id") == compID and
cif::Key("pdb_ins_code") == iCode))
{
result = r.get("asym_id", "seq_id", "mon_id");
break;
}
for (auto r : db["pdbx_nonpoly_scheme"].find(
cif::Key("pdb_strand_id") == asymID and
cif::Key("pdb_seq_num") == seqID and
cif::Key("pdb_mon_id") == compID and
cif::Key("pdb_ins_code") == iCode))
{
result = r.get("asym_id", "ndb_seq_num", "mon_id");
break;
}
}
return result;
}
std::string Structure::insertCompound(const std::string &compoundID, bool isEntity)
{
using namespace cif::literals;
......@@ -2059,8 +1753,6 @@ void Structure::removeAtom(Atom &a)
}
mAtoms.erase(remove(mAtoms.begin(), mAtoms.end(), a), mAtoms.end());
updateAtomIndex();
}
void Structure::removeResidue(const std::string &asym_id, int seq_id)
......
test/unit-test.cpp
......@@ -34,6 +34,7 @@
#include "cif++/BondMap.hpp"
#include "cif++/Cif++.hpp"
#include "cif++/CifValidator.hpp"
#include "cif++/CifParser.hpp"
namespace tt = boost::test_tools;
......@@ -1825,18 +1826,38 @@ BOOST_AUTO_TEST_CASE(output_test_1)
{
auto data1 = R"(
data_Q
_test.text "stop_the_crap"
loop_
_test.text
"stop_the_crap"
'and stop_ this too'
'data_dinges'
'blablaglobal_bla'
boo.data_.whatever
)"_cf;
auto &db1 = data1.firstDatablock();
auto &test1 = db1["test"];
BOOST_CHECK_EQUAL(test1.size(), 1);
struct T {
const char *s;
bool q;
} kS[] = {
{ "stop_the_crap", false },
{ "and stop_ this too", false },
{ "data_dinges", false },
{ "blablaglobal_bla", false },
{ "boo.data_.whatever", true }
};
BOOST_CHECK_EQUAL(test1.size(), sizeof(kS) / sizeof(T));
size_t i = 0;
for (auto r : test1)
{
const auto &[text] = r.get<std::string>({"text"});
BOOST_CHECK_EQUAL(text, "stop_the_crap");
BOOST_CHECK_EQUAL(text, kS[i].s);
BOOST_CHECK_EQUAL(cif::isUnquotedString(kS[i].s), kS[i].q);
++i;
}
std::stringstream ss;
......@@ -1847,11 +1868,12 @@ _test.text "stop_the_crap"
auto &db2 = data2.firstDatablock();
auto &test2 = db2["test"];
BOOST_CHECK_EQUAL(test2.size(), 1);
BOOST_CHECK_EQUAL(test2.size(), sizeof(kS) / sizeof(T));
i = 0;
for (auto r : test2)
{
const auto &[text] = r.get<std::string>({"text"});
BOOST_CHECK_EQUAL(text, "stop_the_crap");
BOOST_CHECK_EQUAL(text, kS[i++].s);
}
}
\ No newline at end of file
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